The high proportion of public land and retention of much of the native vegetation and habitats of the region, means that much of the biodiversity of East Gippsland is exposed to lower levels of threat from changed land use than elsewhere in Victoria. 

In the lowlands and regions cleared for agricultural production, habitats can become fragmentated, whilst pressures from recreational impacts from tourism and recreational pursuits can affect species and habitats, particularly in popular seaside destinations. 

Over much of the rest of the East Gippsland region threats to biodiversity arise from:

Climate change

Increased hot and dry conditions will mean an increase in the frequency and severity of bushfires. If fires occur more frequently than habitats and animal populations can recover, then long term impacts to population viability can be expected. In 2019−20, bushfires affected over 56% of the East Gippsland region, burning a large proportion of the native vegetation and killing or displacing large numbers of animals. The full extent of the impact and recovery from this event is not yet fully understood. A range of bushfire recovery programs have been implemented following the fires.

Alpine areas are highly vulnerable to climate change impacts with reduced snowfall and an increase in the altitude of snow fall. Plants that require periods of chilling to complete lifecycles may not survive.

Many of the impacts to flora and fauna are difficult to predict exactly, although it is expected that gradual changes in temperature and rainfall may see changes in the composition of vegetation communities as more resilient species cope in a warmer and drier climate. There may be an increase in pest plants and animals that are more adaptable to changing conditions. Fauna species may experience changes in behaviour, abundance and distribution as well as potential shifts in regular cycles such as migration or breeding.

Pest plants and animal

Despite much of East Gippsland retaining native vegetation cover, there are still areas of priority weeds and a number of significant pest animal threats to biodiversity. 

• Weeds have the potential to transform important vegetation communities and natural systems, drastically altering their form and function. Riparian weeds like willows have to potential to invade waterways, outcompeting native species, altering water temperature and chemistry, and changing the physical form of streams. Climbing and or shade tolerant weeds can impact rainforest communities, impacting canopy trees and out competing native groundcover species. In coastal ecosystems salt tolerant invasive plants can spread across wide areas of the wild coastlines in East Gippsland altering sand movement and dune formation, and outcompeting native species that stabilise our coastline.
• Horses remain a significant threat in alpine areas. Damage to vegetation communities (including threatened communities and species) is a common impact through overgrazing and trampling, which leads to erosion and water quality impacts to fragile ecosystems such as wetlands and peatlands in alpine areas, particularly where horse numbers are high. 
• Deer are a significant threat across all landscapes in the region causing damage to vegetation communities, threatened plant species and resulting in loss and degradation of habitat for native animals. Deer have the potential to severely impact  alpine wetlands and streams, stands of rainforest, and fragile coastal systems through their browsing, rubbing and wallowing behaviours.
• Pigs also represent a significant threat, particularly in the Upper Snowy, Cobberas and Monero Tablelands. In these areas impacts are greatest in alpine peatlands due to upturning of soils and subsequent weed invasion, and the risk of incursions from cross border areas is ongoing particularly along the Snowy River corridor. 
• Introduced predators such as foxes and cats remain a threat to wildlife including birds, frogs, reptiles and native mammals and the ecosystems that these native species influence (for example the role of potoroos as ecosystem and soil engineers, and quolls as native predators). predators can significantly impact on population of resident and migratory shore and water birds along our coast and estuaries, and continue to impact critical weight range mammals the forested areas across East Gippsland.